dev > main for 3.3.0 release

.github/actions/create-lint-wf/action.yml

@@ -49,7 +49,7 @@ runs:
     # Remove TODO statements
     - name: remove TODO
       shell: bash
-      run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+      run: find nf-core-testpipeline -type f -exec sed -i 's#TODO nf-core:##g' {} \;
       working-directory: create-lint-wf
 
     # Uncomment includeConfig statement
@@ -64,12 +64,6 @@ runs:
       run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
       working-directory: create-lint-wf
 
-    # Add empty ro-crate file
-    - name: add empty ro-crate file
-      shell: bash
-      run: touch nf-core-testpipeline/ro-crate-metadata.json
-      working-directory: create-lint-wf
-
     # Run nf-core pipelines linting
     - name: nf-core pipelines lint
       shell: bash
@@ -88,7 +82,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+      uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

.github/snapshots/adaptivecard.nf.test.snap

@@ -0,0 +1,109 @@
+{
+    "-profile test": {
+        "content": [
+            4,
+            null,
+            [
+                "fastqc",
+                "fastqc/SAMPLE1_PE_1_fastqc.html",
+                "fastqc/SAMPLE1_PE_1_fastqc.zip",
+                "fastqc/SAMPLE1_PE_2_fastqc.html",
+                "fastqc/SAMPLE1_PE_2_fastqc.zip",
+                "fastqc/SAMPLE2_PE_1_fastqc.html",
+                "fastqc/SAMPLE2_PE_1_fastqc.zip",
+                "fastqc/SAMPLE2_PE_2_fastqc.html",
+                "fastqc/SAMPLE2_PE_2_fastqc.zip",
+                "fastqc/SAMPLE3_SE_1_fastqc.html",
+                "fastqc/SAMPLE3_SE_1_fastqc.zip",
+                "fastqc/SAMPLE3_SE_2_fastqc.html",
+                "fastqc/SAMPLE3_SE_2_fastqc.zip",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_plots/png/general_stats_table.png",
+                "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/testpipeline_software_mqc_versions.yml"
+            ],
+            [
+                "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46",
+                "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50",
+                "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870",
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110",
+                "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.03.1"
+        },
+        "timestamp": "2025-05-07T13:52:10.350817122"
+    }
+}

.github/snapshots/changelog.nf.test.snap

@@ -0,0 +1,109 @@
+{
+    "-profile test": {
+        "content": [
+            4,
+            null,
+            [
+                "fastqc",
+                "fastqc/SAMPLE1_PE_1_fastqc.html",
+                "fastqc/SAMPLE1_PE_1_fastqc.zip",
+                "fastqc/SAMPLE1_PE_2_fastqc.html",
+                "fastqc/SAMPLE1_PE_2_fastqc.zip",
+                "fastqc/SAMPLE2_PE_1_fastqc.html",
+                "fastqc/SAMPLE2_PE_1_fastqc.zip",
+                "fastqc/SAMPLE2_PE_2_fastqc.html",
+                "fastqc/SAMPLE2_PE_2_fastqc.zip",
+                "fastqc/SAMPLE3_SE_1_fastqc.html",
+                "fastqc/SAMPLE3_SE_1_fastqc.zip",
+                "fastqc/SAMPLE3_SE_2_fastqc.html",
+                "fastqc/SAMPLE3_SE_2_fastqc.zip",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_plots/png/general_stats_table.png",
+                "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/testpipeline_software_mqc_versions.yml"
+            ],
+            [
+                "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46",
+                "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50",
+                "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870",
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110",
+                "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.03.1"
+        },
+        "timestamp": "2025-05-07T13:52:01.993722854"
+    }
+}